From 2aca12035e9f2dcbdd404b3e578dc59bbf5a539e Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 10 Jul 2024 20:22:35 +0200 Subject: [PATCH] Update config control_method to working --- .../my_control_method/config.vsh.yaml | 27 ++++++++++++------- 1 file changed, 17 insertions(+), 10 deletions(-) diff --git a/src/control_methods/my_control_method/config.vsh.yaml b/src/control_methods/my_control_method/config.vsh.yaml index bba79d9..2438332 100644 --- a/src/control_methods/my_control_method/config.vsh.yaml +++ b/src/control_methods/my_control_method/config.vsh.yaml @@ -8,20 +8,27 @@ __merge__: ../../api/comp_control_method.yaml # A unique identifier for your component (required). # Can contain only lowercase letters or underscores. -name: my_control_method +name: logistic_regression # Metadata for your component info: # A relatively short label, used when rendering visualisations (required) - label: My Control Method + label: Logistic Regression # A one sentence summary of how this method works (required). Used when # rendering summary tables. - summary: "FILL IN: A one sentence summary of this method." + summary: "Logistic Regression with 100-dimensional PCA coordinates estimates parameters for multivariate classification by minimizing cross entropy loss over cell type classes." # A multi-line description of how this component works (required). Used # when rendering reference documentation. description: | - FILL IN: A (multi-line) description of how this method works. - # Which normalisation method this component prefers to use (required). + Logistic Regression estimates parameters of a logistic function for + multivariate classification tasks. Here, we use 100-dimensional whitened PCA + coordinates as independent variables, and the model minimises the cross + entropy loss over all cell type classes. + + reference: "hosmer2013applied" + repository_url: https://github.com/scikit-learn/scikit-learn + documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html" + # Which normalization method this component prefers to use (required). preferred_normalization: log_cp10k # Component-specific parameters (optional) @@ -43,12 +50,12 @@ resources: engines: # Specifications for the Docker image for this component. - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 + image: ghcr.io/openproblems-bio/base_python:1.1.0 # Add custom dependencies here (optional). For more information, see # https://viash.io/reference/config/engines/docker/#setup . - # setup: - # - type: python - # packages: scib==1.1.5 + setup: + - type: python + packages: scikit-learn runners: # This platform allows running the component natively @@ -56,4 +63,4 @@ runners: # Allows turning the component into a Nextflow module / pipeline. - type: nextflow directives: - label: [midtime,midmem,midcpu] + label: [midtime,midmem,lowcpu]